rs1053639
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_019058.4(DDIT4):c.*95T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 1,395,196 control chromosomes in the GnomAD database, including 106,227 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.37 ( 11752 hom., cov: 32)
Exomes 𝑓: 0.38 ( 94475 hom. )
Consequence
DDIT4
NM_019058.4 3_prime_UTR
NM_019058.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.91
Genes affected
DDIT4 (HGNC:24944): (DNA damage inducible transcript 4) Predicted to enable 14-3-3 protein binding activity. Involved in defense response to virus; negative regulation of TOR signaling; and response to hypoxia. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDIT4 | NM_019058.4 | c.*95T>A | 3_prime_UTR_variant | 3/3 | ENST00000307365.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDIT4 | ENST00000307365.4 | c.*95T>A | 3_prime_UTR_variant | 3/3 | 1 | NM_019058.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.374 AC: 56809AN: 151936Hom.: 11730 Cov.: 32
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GnomAD4 exome AF: 0.379 AC: 471182AN: 1243142Hom.: 94475 Cov.: 18 AF XY: 0.379 AC XY: 232069AN XY: 612138
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GnomAD4 genome ? AF: 0.374 AC: 56863AN: 152054Hom.: 11752 Cov.: 32 AF XY: 0.388 AC XY: 28840AN XY: 74322
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at